+Open data
-Basic information
Entry | Database: PDB / ID: 6bzf | |||||||||
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Title | Structure of S. cerevisiae Zip2:Spo16 complex, C2 form | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / XPF-ERCC1 Meiosis Recombination | |||||||||
Function / homology | Function and homology information regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination ...regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination / reciprocal meiotic recombination / protein sumoylation / condensed nuclear chromosome / nucleotide binding / mitochondrion Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.286 Å | |||||||||
Authors | Arora, K. / Corbett, K.D. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding. Authors: Arora, K. / Corbett, K.D. #1: Journal: Biorxiv / Year: 2018 Title: Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation Authors: Arora, K. / Corbett, K.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bzf.cif.gz | 655.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bzf.ent.gz | 542 KB | Display | PDB format |
PDBx/mmJSON format | 6bzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bzf_validation.pdf.gz | 512.6 KB | Display | wwPDB validaton report |
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Full document | 6bzf_full_validation.pdf.gz | 546.7 KB | Display | |
Data in XML | 6bzf_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 6bzf_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzf ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzf | HTTPS FTP |
-Related structure data
Related structure data | 6bzgSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/538 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Sporulation-specific protein ... , 2 types, 4 molecules AECG
#1: Protein | Mass: 25380.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122 #3: Protein | Mass: 25353.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122 |
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-Protein , 3 types, 4 molecules BDFH
#2: Protein | Mass: 24630.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061 |
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#4: Protein | Mass: 24657.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061 |
#5: Protein | Mass: 24603.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061 |
-Non-polymers , 1 types, 224 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.6 / Details: 1.4 M Na-K phosphate pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.286→100 Å / Num. obs: 95052 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rsym value: 0.091 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.286→2.33 Å / Num. unique obs: 10085 / CC1/2: 0.328 / Rsym value: 1.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BZG Resolution: 2.286→57.093 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.286→57.093 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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